Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

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Genome Duplication Increases Meiotic Recombination Frequency: A Saccharomyces cerevisiae Model

Genetic recombination characterized by reciprocal exchange of genes on paired homologous chromosomes is the most prominent event in meiosis of almost all sexually reproductive organisms. It contributes to genome stability by ensuring the balanced segregation of paired homologs in meiosis, and it is also the major driving factor in generating genetic variation for natural and artificial selection. Meiotic recombination is subjected to the control of a highly stringent and complex regulating process and meiotic recombination frequency (MRF) may be affected by biological and abiotic factors such as sex, gene density, nucleotide content, and chemical/temperature treatments, having motivated tremendous researches for artificially manipulating MRF. Whether genome polyploidization would lead to a significant change in MRF has attracted both historical and recent research interests; however, tackling this fundamental question is methodologically challenging due to the lack of appropriate methods for tetrasomic genetic analysis, thus has led to controversial conclusions in the literature. This article presents a comprehensive and rigorous survey of genome duplication-mediated change in MRF using Saccharomyces cerevisiae as a eukaryotic model. It demonstrates that genome duplication can lead to consistently significant increase in MRF and rate of crossovers across all 16 chromosomes of S. cerevisiae, including both cold and hot spots of MRF. This ploidy-driven change in MRF is associated with weakened recombination interference, enhanced double-strand break density, and loosened chromatin histone occupation. The study illuminates a significant evolutionary feature of genome duplication and opens an opportunity to accelerate response to artificial and natural selection through polyploidization.     

Chloroplast DNA polymorphism in different types of cytoplasmic male sterile rice

The lengths of open reading frame (ORF)100 and ORF29-TrnC^GCA, the intronic sequence of rps16 and the transcribed spacer of TrnT^UGU-TrnL^UAA in chloroplast from different lines of cytoplasmic male sterility (CMS) rice were studied using indica types, japonica types and common wild rice as controls. The results show that the lengths of ORF100 and ORF29-TrnC^GCA in CMS lines are similar to those of typical indica. The sequences of the rps16 intron and the TrnT^UGU-TrnL^UAA spacer in sporophyte sterile types (wild-abortive type, Yinshui type and K type) are almost the same, and they also share a molecular marker of GTTGAG at nucleotide positions 220–225 in the rps16 intron. Therefore, it is speculated that the source of these three types is the same. In contrast, a gametophyte sterile type, Yuetai A does not contain such a GTTGAG sequence in the rps16 intron and has a unique G at position 595, which may works as a molecular marker distinguishing the sporophyte sterile type from the gametophyte sterile type. Based on the observation that CMS rice has much lower cytoplasmic polymorphism than indica, japonica and wild rice, it is concluded that CMS rice lack cytoplasm diversity. Therefore, it is important to introduce new sources of cytoplasm into hybrid rice.